Making his way home
by mentalmichael
Summary: John returns from a mission offworld a changed man
1. Chapter 1

**Making his way home**

**Summary: I suck at summaries**

**Spoilers: Probably nothing much, but anything from season 2 is fair game**

**Disclaimer: I don't own Stargate Atlantis. If I did, there would be an episode where this happened:**

**Chapter 1**

Lt. Colonel John Sheppard strolled into Elizabeth's office. As usual, he thought, she was too busy working to even notice.

"Elizabeth? You in there?" She looked up from her work, a small smile brightening her face.

"John. Shouldn't you be going off-world?"

"Yeah, but not for like 5 minutes." He let out a deep breath as he sat down. "I actually needed to talk to you."

"Is there something wrong?" she asked, concerned.

"No, not really…" he trailed off. Elizabeth continued to stare at him, and he shifted uncomfortably.

"John?"

"Ok, umm, do you want to have dinner with me?" He regretted saying the words as soon as they left his mouth. They often ate together, but he had never asked so formally. Hell, on occasion he had had to literally drag her out of the office to get some food, but he had never actually asked her to dinner. She leaned forward in her chair, tilting her head slightly, with an amused expression on her face.

"Colonel Sheppard, are you asking me on a date?"

"Well, that kinda depends." She raised an eyebrow and grinned slightly

"Depends on what?"

"Well, you could call it dinner between two friends, or it could be a date." He cringed, waiting for a rejection.

"Sure." He looked up.

"What?" She smiled at him.

"I said sure, I'd love to have dinner with you. Now, I have a lot of work to do, and you have to go off-world."

"So…. It's a date?" She sighed and rolled her eyes.

"Yes, it's a date. Unless there was anything else?" When he still made no move to leave, "I'll see you later John." He finally got the hint and stood, unable to control the smile on his face. As he started to leave the room, she called out after him.

"Hey John." He turned back. "Where are you taking me?" He smiled and shrugged.

"Mum's the word."

He continued through the control room, and walked down the stairs to the gate room, fighting the urge to jump down them (Carson was already annoyed with him for sneaking out of the infirmary after the retrovirus incident, he probably wouldn't be gentle with a sprained ankle.) His team was waiting at the bottom of the stairs. Unsurprisingly, Rodney had to make a comment.

"Colonel. How nice of you to join us."

"Mckay. Everyone ready?" Teyla nodded

"We are Colonel. Is everything alright?"

"What do you mean?" Teyla smiled slightly.

"Normally you do not speak to Dr Weir immediately before a mission."

"Yeah, well, I just needed to clear something up. Alright, let's go."

As the team moved towards the dialling gate, Rodney moved next to Teyla, and started to mutter to her.

"You don't think that those two have finally…….?"

"I don't know. If they have, it is a private matter, and not one for open discussion." She paused, then leaned a bit closer. "Although obviously if that did happen it would be a great relief to anyone making bets on the matter, don't you agree Rodney?"

He spluttered quietly.

"How did you find out?"

She just smiled enigmatically.

As the team walked towards the gate, John glanced over to her office. She was sitting in her chair, eyes fixed on his. He smiled, and blew her a kiss as he walked through the gate. He wasn't there to see her hand rise to stroke her cheek, before she snapped out of it and returned to life as leader of Atlantis.

John and his team stepped out of the gate into a small clearing in a large forest.

"Alright Mckay, you're the science geek. Go find us a ZPM."

"I resent that. And if you'd been listening in the briefing rather than staring at Elizabeth then you would know that-"

"I was not staring! Ronon, back me up on this."

"Uh, I didn't really notice." Mckay broke back in

"Of course not you were probably distracted by the chocolate bar in your hand. Look my point is that the energy pattern is not that of a ZPM, but it is still worth investigating. We just need to lock it down."

John sighed deeply, and shook his head.

"Alright, let's lock it down. The UAV showed no intelligent life anywhere near here, and there weren't any signs of big animals, so we'll split up. Teyla and Ronon, you two go together, and I'll take Dr Freud here." Both Teyla and Ronon looked perplexed. "Dr Freud. He was a psychologist… you know what? Forget it. Let's just get this over with. Stay in radio contact." With that, he turned and headed off. Mckay soon caught up.

"Eager to get back to Atlantis?" John kept walking

"As a matter of fact, yes. And yes, before you ask, Elizabeth and I are having dinner together."

"Oh. That's nice. I myself have a date with Katie." Sheppard smiled at him (only slightly sarcastically)

"That's nice too. Now could we find the damn energy source so we can go home?"

Two hours later, John reflected on how overly optimistic he had been.

"Alright, I'm just about ready to call this one. Teyla and Ronon, have you had any luck?"

"I'm afraid not Colonel. We have been unable to isolate the energy. It's as if it's coming from everywhere at once."

"Yeah, Mckay's having the same problem." He was interrupted by a fit of swearing. "He's dealing with it pretty well though. We'll see you back at the gate."

Some time later, Teyla and Ronon emerged into the clearing.

"That's weird." Teyla looked over to Ronon.

"What is it Ronon?"

"We must've covered more ground than Mckay and Sheppard. So why aren't they here already?"

Teyla frowned, and tapped her radio.

"Colonel Sheppard, where are you? Colonel Sheppard? Doctor Mckay, please respond." She looked anxiously at Ronon, who shrugged.

"If they were attacked we should've heard it, but maybe not. We won't be able to search for them on our own." Teyla nodded, her face grim.

"Then we must dial Atlantis, and ask Dr Weir to send more people." But first, she reflected silently, she would have to tell the Doctor that Colonel Sheppard was once again in trouble.

"Unscheduled offworld activation!" Elizabeth was up and out of her chair almost before the watch officer had finished speaking.

"Receiving a radio signal. It's Telya."

"Teyla, this is Doctor Weir. What's your status?"

"We have lost contact with Dr Mckay and Colonel Sheppard. This is a large forest, and we need reinforcements to search it properly." Elizabeth's heart clenched, but she managed to keep her voice under control.

"Ok, I'll have Major Lorne assemble a team."

"A puddle jumper would also help, it's sensors should be able to penetrate the vegetation."

"They're on their way. Do you think that…" She could hear Teyla sigh over the radio

"I do not know. Neither Ronon nor I heard anything, the last contact was around an hour ago, when the Colonel told us he would see him at the gate. A search may be premature, but" she was cut off

"No, Teyla, you did the right thing. The others will be with you as soon as possible."

"Thank you Doctor Weir. We will find them." As the gate disconnected Elizabeth tapped her radio.

"Major Lorne? We've lost contact with Dr Mckay and Colonel Sheppard. I need you to assemble a search team. Take as many men as you need, and a puddle jumper"

"Copy that. We'll be ready in 5." Elizabeth turned to the watch officer.

"Send them out as soon as they're ready." He nodded in response. She turned, and walked slowly out onto their balcony, shivering slightly as the cold air hit her. She leaned on the railings.

"Damnit John. You'd better be home for dinner."

To be continued…..


	2. Chapter 2

**Chapter 2**

Major Lorne, Teyla, and Ronon moved through the dense forest.

"This is a waste of time." Ronon remarked sourly. "We've already searched this area."

"Maybe so, but the jumper's searching further away, so we're going to search this area again!" snapped Lorne

"I agree," interrupted Telya. "We must not stop until we find Colonel Sheppard and Doctor Mckay."

"Yeah, if we don't find Sheppard Weir'll have our asses." Lorne commented.

"What about Mckay?"

"Well yeah obviously she's really worried about Dr Mckay, but let's face it, Colonel Sheppard is…." He was cut off by a small beep. He glanced around, confused, then looked down at the life-signs detector in his hands

"We've got something. One life sign, 20 metres that way." They moved quickly through the trees, breaking into a run as they saw a body slumped on the ground.

"Mckay!" The doctor lay unconscious.

"Sgt Malarky, this is Lorne. Dial Atlantis and have the Doc stand by, we've found Mckay unconscious and are bringing him in." Ronon picked Mckay up and slung him over one shoulder. Teyla followed the three men, looking confused.

"I do not understand. We had already searched the area. How did we not find him?"

"If he had been there, we would've found him. Someone put him there for us to find" said Ronon. Lorne shook his head.

"That's impossible, the UAV showed no signs of life anywhere near this forest, and it's huge."

"Well then how did he get here?"

SGA-SGA-SGA

Elizabeth stood in the control room. Major Lorne was on the screen in front of her as Doctor Mckay was carried through the gate.

"I don't understand Major, you're saying that someone put him there? Who?" On the screen, Lorne's face grimaced.

"I don't know Doc, but so far we haven't seen anyone, and the puddle jumpers haven't detected anything either. And so far, there's no sign of Colonel Sheppard."

Elizabeth nodded slowly, trying to keep a straight face. From the look she was getting from Major Lorne, it was clear she was failing.

"Alright Major, keep looking."

She walked slowly out of the control room, and back into her office. On the desk was a stack of reports which needed to be read. Somehow, she doubted she would get through any until he was home and safe.

SGA-SGA-SGA

Two days later, Elizabeth was once again standing on the balcony, staring out across the city. Rodney was still unconscious, but Carson said he was "stable" They were still searching for John, but so far there was nothing. Every time the gate activated her chest clenched, she was getting headaches from the stress. And every damn time the gate opened she had to put on her poker face and try to stop the pain from showing.

"Unscheduled off-world activation!" Elizabeth sighed, and walked into the control room.

"Receiving an IDC. It's Major Lorne"

"Lower the shield!" She couldn't avoid the note of excitement creeping into her voice. As she looked over to the gate, she saw Major Lorne, Teyla and Ronon, and other members of the search party come through. Then she saw him. John was unconscious, carried between two soldiers.

"Oh my God." She ran down the stairs to Lorne.

"Where was he?"

"He was lying in the open less than 500 metres from the gate. There's no way we could've missed him!" Lorne exclaimed, clearly frustrated.

"Alright, get him to the infirmary. We'll debrief in an hour." She turned and walked away, trying to keep herself under control. She walked out onto the balcony, and once again leaned on the railing. She stood there, until a voice quietly intruded.

"Dr Weir?" turning, she saw Teyla.

"Dr Weir, is everything alright?" Elizabeth smiled slightly, painfully aware of the tears trickling down her cheek.

"Yes I'm alright Teyla. It's just….been a long two days."

"Yes." Teyla turned as if to leave, then paused, and turned back. "May I ask you something?" Elizabeth nodded. "Did something happen between yourself and Colonel Sheppard?" Elizabeth blushed, and looked away.

"No, but we had arranged to have dinner. I was hoping that something might happen."

Teyla smiled sympathetically.

"Well, perhaps they will both wake up soon. As I recall, Rodney mentioned that he had a date as well."

"Yeah, Dr Brown has barely left the infirmary in two days. But don't tell him that when he wakes up."

Teyla smiled broadly

"I would never dream of it." As she turned to go, Elizabeth looked up.

"Teyla? Thanks."

SGA-SGA-SGA

"I still don't understand it. How could he have just appeared there?" Elizabeth looked over to Major Lorne, sitting at the conference table.

"I don't know Doc, but he did. We'd walked over that spot dozens of times, and then he was just… there." Suddenly, Carson's voice emerged from her radio.

"Elizabeth it's Carson. We're getting rapid eye movement here. I think they're starting to wake up." Her head jerked up

"I'll be right there. Major, consider this debriefing suspended." She turned, and hurried towards the infirmary. On the way, she met Teyla and Ronon.

"You've heard?"

Ronon shrugged.

"I think the whole city's heard. You people love to talk." He stopped as they entered the infirmary. Carson waved them over to where Rodney lay.

"He just woke up. Said the last thing he remembered was walking in the forest with Colonel Sheppard."

"Is he going to be alright?" Teyla asked.

"Aye, I think so. He's sleeping normally."

"Doctor Beckett! Colonel Sheppard is waking up!" A nurse called out.

Elizabeth pushed past the surprised doctor, reaching Johns bed as his eyes started to open. He looked around, confused, then his eyes focused on her face. He stared for a moment.

Then he started to scream.

Oh don't you just love a cliff-hanger? I know I do! I also love reviews by the way...


	3. Chapter 3

**Chapter 3**

Elizabeth leaned forwards to grab John's arm, but he hit it away as he jumped out of the bed, pressing himself into a corner. His eyes were wild, almost feral as they darted from person to person. Dr Beckett stepped forwards.

"Calm down Colonel, you're in the infirmary." John's head started to shake; his voice was rough and full of anger.

"No." Elizabeth moved slowly past Carson, gesturing to Ronon and Teyla to stay back. His eyes locked on to hers, and she had to stop from gasping. His eyes were so full of pain and anger, his entire face was contorted into a grimace.

"Stay away from me" he snapped, biting off the words.

"John, we just want to help you."

"No. This is wrong. This is a trick. You're all dead!" Suddenly, he leapt at Elizabeth, grabbing her by the throat and hurling her towards Ronon and Teyla, leaving all three of them sprawled on the floor. He punched Carson, sending him spinning onto Rodney's bed, who looked on, shocked and powerless. John ran out of the infirmary, leaving his shocked friends behind.

Elizabeth was the first to recover. She rose slowly to her feet, breathing deeply as nurses rushed towards them.

"I'm fine, look after Dr Beckett. Ronon, Teyla, put together search teams. They are to be armed only with stunners." Ronon pulled Teyla to her feet.

"Yes Dr Weir." Elizabeth stared after them as they left, then she tapped her radio.

"Control Room, this is Weir. Lock down the city. All non-military personnel are to stay where they are, all military troops not needed by Teyla and Ronon are to secure the checkpoints."

"Right away ma'am. What's happening?" Elizabeth ran one hand through her hair.

"Colonel Sheppard has just escaped from the infirmary. He appears confused, and is violent. We need to find him. Have Zelenka locate him on the bio-scanner, and despatch teams as soon as you locate him." With that, she turned off the radio. As she turned to leave, Rodney spoke.

"Elizabeth?" She whirled around

"WHAT?" The nurses tending to Dr Beckett and the other patients in the infirmary all looked around as he jumped.

"I just wanted to say…. We'll get him." Elizabeth swallowed away the lump in her throat, and replied in a more normal voice.

"I'm sorry. You're right, we will get him." She left the infirmary and ran to the control room, passing soldiers already covering transporters and key rooms in the central tower. When she arrived, she saw Teyla, Ronon, Major Lorne, and dozens of soldiers standing in the gate room.

"Report." They looked at her strangely. She realised how cold and military her voice sounded. "I mean, what's happening?" Dr Zelenka pressed a few control crystals on the bio-scanner.

"One moment, I just need to...there!" They all crowded round the device. There were hundreds of dots spread out across the city, but most were staying still. Only one was moving quickly away from the central areas.

"That has to be him." Major Lorne remarked. "Oh shit!"

"What is it Major?" Elizabeth asked, wondering what else could have gone wrong.

"Look, he's stopped. Unless I'm reading this wrong, he's inside one of the secondary armouries."

"Jesus." Elizabeth pushed away from the console. "Put me on city-wide."

"John? This is Elizabeth. I know you can hear me, and I know that you're scared, and confused. We just want to help you John, please. Just walk back to the control room; we'll meet you on the way. Please." The dot on the screen didn't move, then it left the armoury, and moved rapidly away, in the direction of the Northern Pier.

"Damn. Where's he going?" She looked around the control room, and saw only confusion. Then Zelenka looked up.

"Wait, he's entering a transporter."

"What?" She turned on the control officer. "I thought you locked them down!"

"I, I did" he stammered. "Sheppard's ancient gene must have overridden the locks."

"Where is he now?" Zelenka looked frustrated.

"I have to reacquire him, one second. Ah, he's..." Zelenka's voice trailed off, his face turning white.

"What is it? Radek?"

"He's, he's heading for the main drive unit at the base of the control tower. Only one reason to go there. If he has C4, he can blow the power regulator systems, then he can use computer to cause energy surge, trigger chain reaction throughout the drive system. The whole city..."

"Oh my God" Lorne breathed as the realisation hit them. Elizabeth turned to him.

"Stop him. Do whatever it takes. Teyla, I want you and Ronon to go with the teams, try and talk him out of it. Ronon" The tall warrior cut her off.

"My gun's already set to stun. I can take him."

"Good. Go get him." They nodded and left the control room.

"Radek, why can't we just shut down power to the drive?" The scientist stared at her for a moment.

"Of course, but it would mean shutting down all main power. The drive systems are permanently interlinked with main ZPM in case of sabotage."

"Radek, this is an emergency. Cut power to the city."

"Ok, done" The lights flickered, then went out. "But he still has C4, lots of it. He can still do damage, cause flooding."

SGA-SGA-SGA

Ronon moved down the darkened hallway. Teyla and Major Lorne followed him closely behind. On the life-signs detector in Major Lorne's hand, two other teams of marines were closing in on the Colonel's position.

Lorne tapped his radio

"Team two, he's heading towards you."

"Copy that, we're holding position... I see him" Then, over the radio they heard "Colonel Sheppard, stop! I said stop godammit! Open fire!" Gunfire echoed around the corridors and through the radio."

"Shit. Let's go!" Ronon yelled over his shoulder as he ran towards the noise. They skidded to a halt as they saw the bodies.

"Doc, get a medical team down here. Sheppard just took out one of our teams. They seem to only be unconscious though. No, shit! Sgt Barrows is down with a shot in the arm, and the chest, but he's breathing ok."

"Understood Major, we're on our way. Catch the poor bugger before he puts anyone else in my infirmary!" Despite the situation, all three laughed

"Copy that. Lorne out."

"Alright, enough of this containment crap. Let's get him." Teyla and Lorne had Wraith stunner pistols, and Ronon had his blaster. They moved away as the medical team arrived.

"Ok, he's about 100 metres down this passageway. Weird, he's just standing there."

"We should approach slowly; we do not want to scare him." Teyla said.

"Agreed, but Ronon, be ready. That blaster works faster than our stunners and we have to take him down if he tries anything."

They moved slowly down the dark corridor, until they came to a triangular intersection. John stood there, a stunner in one hand, the C4 remote detonator in the other, illuminated by their flashlights. A P90 lay abandoned by his feet. Teyla moved forward, drawing his attention away from Ronon, whose hand was right next to his holster.

"Colonel Sheppard, please put them down." He didn't answer, didn't even blink. He just kept staring at them.

"Colonel, you do not wish to hurt us, and you do not want to destroy Atlantis."

"Atlantis is gone. This is a trick, and I'm going to end it." His voice was a low rasp, devoid of any human emotion save rage.

"Colonel, I don't know what you've been through, but this is no trick. If you press that button, people will die."

"No. You're already dead." He suddenly raised his stunner and fired, catching Lorne off guard and knocking him out. Teyla was also surprised, but Ronon drew his blaster in one swift move and fired at the hand holding the detonator. John dropped the detonator, and with a roar of rage hurled himself onto Ronon, hitting him with fists, feet, elbows. They dropped to the ground, still struggling. In the few seconds it took for Ronon to kick John away, Teyla had recovered, and shot John twice with the stunner. A shocked look crossed his face, as he tried to rise to his feet, then collapsed back to the ground, unconscious. Teyla helped Ronon to his feet.

"Nice shot."

"Likewise. Dr Weir, this is Teyla. We have captured Colonel Sheppard. I suggest that a demolitions team find and disarm the explosives."

"They're already on their way. Good work Teyla."

SGA-SGA-SGA

John once again lay in the infirmary bed. This time, however, he was in restraints. Two guards stood inside the infirmary, and another two watched the corridor outside. After seeing what the colonel had done to an entire security team, no one thought it was overkill.

"What's wrong with him?" Elizabeth asked, turning away from John to look at Carson.

"I don't know. We've run all the tests, this is our John Sheppard. The DNA is a match. I'm sorry Elizabeth, but at this point I have no idea what to do."

She nodded slowly, her face a grim mask of control.

"Let me know the second he wakes up. Maybe he'll be more willing to talk..."

Carson smiled sadly and nodded.

"Aye, maybe. Now you go and get some rest, doctor's orders."

Elizabeth walked out of the infirmary, and walked slowly and calmly to her quarters, greeting expedition members she encountered on the way. The mask of control lasted until she made it inside her room. Then she started to scream. It started out low, almost a moan, and then rose to an expression of all the anger and loss she felt inside. She grabbed a chair, and flung it away from her, sending it crashing into her bed. Stacks of paper were sent flying as she violently swept her desk clean. She collapsed onto the bed, scarcely able to breath, gulping for air around the sobs as she rhythmically pounded her sheets.

Slowly she came back to reality, the wave of energy spent. She looked around the room, seeing what she had done. She was numb, hollowed out and empty. She couldn't move, and couldn't fight the numbing tiredness that drifted through her as she slowly slipped into dreams.

To be continued...

So, what do you think? Reviews feed creativity!


	4. Chapter 4

**Chapter 4**

Elizabeth woke slowly, emerging from confused dreams of the previous day. John grabbing her throat, hurling her away. The manic gleam in his eyes. As she slowly sat up, she realised she was still wearing her clothes from the day before. She looked around the room, eyes widening at the damage she'd done. Looking at her clock, she realised she only had ten minutes before her first briefing of the day. She hurriedly showered and changed clothes, before leaving the chaos of her room behind. Walking towards the control room, she bumped into Zelenka and Rodney, in the middle of what they would probably describe as a "heated debate" and what everyone else would call a flaming row.

"No! I am telling you, we did all the scans we could, even the puddle jumper's sensors couldn't lock it down!"

"Yes, and I am telling you Rodney, this is because the field is too expansive! The energy you detected was very weak but could be found over the entire forest! There is something there!"

"Even so, we couldn't find anything with the jumper, so it doesn't really matter does it!"

"Gentlemen!" Both men fell silent as they saw Elizabeth. "Rodney, what are you doing out of the infirmary?"

"Oh, Carson said I was fine and should get back to work." She tilted her head to one side slightly

"Really?"

"Actually, Dr Beckett said that Rodney was making a fuss about nothing and that he was too busy dealing with Colonel Sheppard to cope with such a cry-baby."

"John's awake?"

Rodney shook his head sadly

"No, Teyla really hit him with the stunner and Carson is keeping him sedated."

Elizabeth nodded, feeling a brief glimmer of hope vanish.

"Right. So what are you two bickering about?"

Rodney glared at Zelenka.

"This genius is convinced that the energy field we detected in the forest is linked to Sheppard's...abduction."

"And you don't agree?"

"No, I just don't see how that helps as the jumper's sensors couldn't isolate the signature. It just spread out over the forest, a few points where it got a bit stronger, but there was nothing around to generate it."

"Then how do you explain it?" Zelenka butted in, as they started to squabble again.

"Okay, stop. Radek, even if you're right, the jumpers can't detect anything."

The scientist nodded rapidly

"Yes, yes, I know. But the Deadalus has Asgard sensors. They are one of the few things that are more advanced than what the Ancients used. Also, if the ship stays in orbit it might be able to, to map out the energy field's radius."

Elizabeth nodded slowly, and tapped her radio.

"Colonel Caldwell? How long will it take to unpack the last of the new supplies from Earth?"

"About two hours, why?"

"Zelenka thinks that the Asgard sensors might be able to locate the source of the energy field on M89-K4X."

"Understood, we'll leave as soon as the supplies are unloaded."

"Good, I'll see you there."

"Doctor?"

Elizabeth rolled her eyes.

"Yes Colonel? Do you really think I'm going to sit by and wait for you to report in? I'm coming with you." She tapped the radio again, ending the conversation.

"Alright, Rodney you're coming with us, I just have a few things to take care of." As she walked away, Zelenka and Rodney exchanged glances.

"She really is worried, isn't she?" remarked the Czech

"Yeah. I think she only just realised how important John is to her."

SGA-SGA-SGA

The Daedalus shot out of hyperspace into orbit around a planet. Looking out of the window, Elizabeth saw the huge forest sprawled across the Southern continent.

"Alright Dr Mckay, let's see if this trip was worth it." Caldwell said in his typically businesslike tone. Rodney moved over to one of the computer consoles.

"Okay, scanning the forest and...woah." Elizabeth moved next to him.

"Woah?"

"Yeah. The sensors have mapped the edges of the energy field. No wonder the hand scanners couldn't localise the field, it covers the whole forest. That's bigger than Atlantis!"

"That's nice Rodney, can you find a source?"

"Yeah I think so, just give me a second. It seems to be deliberately designed to deflect sensors like a less advanced version of the puddle jumper's cloaking field, but the Asgard sensors are much more advanced than anything this galaxy has to offer so... there!" On the screen, the shield melted away.

"What is that?" Breathed Caldwell, standing behind them both.

"It looks like a cave network, but it's massive. That one cavern must be the size of Time Square! Hold on, I'm detecting life-signs. There're humans down there!"

"Are you sure?"

"Positive, looks like a couple of thousand of them."

Elizabeth nodded.

"Colonel, I'm going down there. Ah!" She raised a hand as he started to protest. "I'll take Lorne and a security team with me, and you can maintain a constant lock on me. If we run into trouble, beam us out."

"Alright."

5 minutes later, Elizabeth, Lorne, Mckay and twenty soldiers stood waiting to be beamed down. Caldwell's voice came over the radio.

"Good luck Doctor, at the first sign of trouble we will beam you out."

Elizabeth closed her eyes, and when she opened them again she was no longer on the Deadalus. She and the others stood in a large cavern. All around her humans wearing silver and gold clothing stared in horror. The soldiers swiftly spread out in a defensive circle, but she noticed that none of the people had any weapons, and they all seemed terrified. She stepped forward.

"My name is Elizabeth Weir. We do not mean you any harm."

"Then why are you here, Doctor?" She turned, and saw a distinguished looking old man. Next to him stood a younger woman with long black hair, wearing silver clothes.

"Doctor? I never said I was a Doctor." The man smiled arrogantly.

"Yes well, we know a lot about you. A lot about you, and about Doctor Mckay, and about Atlantis."

"What?" She took an unconscious step forward, and the troops shifted, some of them aiming at the man.

"I ask again. Why are you here?"

Elizabeth's eyes narrowed

"We are here because you kidnapped two of my men and held them for hours. I want to know why."

"I am sorry, but we cannot help you. We are not permitted to interact with outsiders. You will leave immediately."

"Really? I don't think so." Her hand rose to her earpiece. "Colonel Caldwell? Prepare to beam a Mark 8 nuke into the cavern."

"Doctor?"

"I'll explain later, just do it."

"Very well, the missile is ready to be beamed down."

The mans face turned from arrogance to fear, and he stepped back. At this, the younger women stepped forward.

"Please, do not. We are a peaceful people, we only wanted to know about your kind."

"Lessa, this is forbidden!" The man snapped.

"They have a right to know what happened, Athar." The man subsided, and Elizabeth nodded sharply at the woman, who continued.

"You must understand, my people have lived in these caves for generations. Free from the threat of the Wraith, we have developed far beyond the normal level of technology for this galaxy. However, our isolation does have its drawbacks. So when travellers come to our planet we... borrow them for a short time." Suddenly Rodney stepped forward.

"You! You brought us down here, attached us to some machine!" Lessa nodded solemnly.

"We have a device which places people in a dream-like state. They relive past experiences, and in doing so we gain information about the galaxy. The process is accelerated so that we gain years of knowledge in a few short hours. Normally we would then return the subjects, and they would leave thinking that they fell asleep or passed out. Before we remove them from the machine we suppress their memories of being brought here. You must understand, we only want to learn, not to cause harm."

"Well evidently something went wrong! Colonel Sheppard has gone mad because of what you did to him!" Rodney stared at her, shocked by the bitterness in her voice. Lessa shook her head sadly.

"No, he is not mad. With both Dr Mckay and Colonel Sheppard we had difficulty removing them from the device. After great difficulty, we were able to remove Dr Mckay, and we transported him to the forest near to your search parties, but Colonel Sheppard proved more difficult to remove. We think it has to do with an unusual gene, which gave their subconscious minds control over our device."

"The ATA gene!" Rodney gasped. Seeing Lessa's blank face, he continued "It allows us to use technology built by the Ancestors. I assume you know who they were?"

"Of course, in fact we integrated some of their technology with the device to make it work! That explains it!"

"And as Colonel Sheppard has a more natural command of the gene, he was harder to remove. Very clever." Rodney smiled, then stopped when Elizabeth glared at him.

"So what actually happened to Colonel Sheppard?"

"Having studied recordings of Colonel Sheppard's memories, I believe that his mind rebelled against the control of the device. Instead of merely reliving memories, the Colonel actually started to create a new reality in his mind, a possible future. Unfortunately, it seems that the future he created was not a happy one."

"Which means?" Elizabeth bit the words off.

"For around 6 months (his timeframe of course) the reality he created seemed fine. Then the Wraith came. Atlantis was destroyed, and the expedition members killed. The machine disconnected when he 'died'. We then returned him to you."

Elizabeth pushed past the soldiers still standing in a defensive circle. She walked towards Lessa until she was only a few inches away.

"You put Colonel Sheppard into a nightmare that he couldn't wake up from until he was dead?"

"Please, we tried to remove his memories, but we failed! We thought it would be best for him to return to his own people, your technology is far more advanced than ours!"

"I should order them to beam the nuke down, but I won't if you come back to Atlantis with us. You will work with our doctors and scientists to cure Colonel Sheppard, and you will be returned here. Agreed?"

Lessa swallowed, her eyes betraying her fear.

"Agreed."

TBC...

That was a really irritating chapter to write for many many reasons, thanks go to Erised for being kind enough to beta it!


	5. Chapter 5

**Chapter 5**

The Deadalus slowly touched down, and Elizabeth, Rodney, Lorne and Lessa were the first off the ship.

"Major, escort our...guest to the infirmary. Tell Carson to work with her." Lorne nodded, and gently led the woman away.

"Rodney... get back to whatever it was you were doing." Rodney nodded, and slowly walked away. Elizabeth turned, and walked back towards her room. Entering it, she was again amazed and frightened by the mess that she had made. She was always the one in control, always. Even when that bastard Kolya was pointing a gun at her, she had kept calm, tried to negotiate. And yet somehow John had managed to slip past all her defences, all her self-control, into her heart. She laughed bitterly as she slumped on her bed. She remembered that look of fear in his eyes when he asked her to dinner, as if she was really going to say no after waiting months for him to make the first move! She sighed and stood up, moving over to her desk. She bent down next to it and picked up her chair.

Twenty minutes later she had finally started on the papers still strewn around her floor when the door chimed. Fighting an urge to scream, she slowly walked over to the door, and opened it to reveal Rodney standing outside looking very nervous.

"Elizabeth. Hi. Mind if I come in?" Elizabeth was slightly confused, but stood aside and let him enter. She regretted it the second he looked around the room, seeing the papers across the floor. He turned to look at her.

"I don't suppose you'd believe me if I said I was... spring cleaning?" she asked as she sank down onto the bed

"No." He sat down next to her. "What's going on Elizabeth? This isn't like you."

"I'm not allowed to be a little untidy?"

He shook his head, frustrated.

"That's not what I meant. Back on the planet, in the city. You threatened to blow them all up. I've, I've never seen that side of you before. I heard Lorne talking to one of the marines, he said you sounded like a soldier. To be honest, you were scary in there."

Elizabeth nodded slowly and looked down at her hands, noticing for the first time how tightly they were clasped together.

"It had to be done. If I hadn't threatened them Lessa would never have offered to come back with us, and we wouldn't be able to help John." The last few words came out as a gasp. Rodney leaned back, shocked.

"I, I didn't realise how important he was to you. I mean, I knew that he had asked you to dinner, but... Look, I'm really not the best person to talk to about this, but do you love him?"

"I... don't know. I could've loved him but now..." her voice trailed away hopelessly. Rodney awkwardly put a hand around her, and started slightly as she leaned towards him.

"For what it's worth, I think John cares for you a lot. We can all see it. When he gets better, maybe you can have that date."

"Yeah. Maybe." She slowly pulled away from Rodney, and smiled gratefully at him. "Thanks Rodney."

"Sure. But I still don't think I'm the one you should talk to about this. Maybe Dr Heightmeir?"

"Rodney, I'm an emotional wreck. I'm not crazy."

SGA-SGA-SGA

Several days later, Elizabeth walked into the infirmary. She looked over to where John still lay sedated in restraints, then turned away.

"Carson, Lessa, you wanted to see me?"

"Aye, Lessa here has been very helpful, and we think we've found something." He glanced over to Lessa who stood quietly (and, Elizabeth realised guiltily, Lessa looked quite scared whenever she was in the room. Evidently Rodney had been right, she was scary in Lessa's city)

"Dr Weir, after examining Colonel Sheppard we have come to the conclusion that there is no way to remove his memories."

"I'm sorry, I thought you said you had found something?"

"Yes. Although we cannot remove those memories, we can make him realise that they are not in fact real."

"How?" Carson stepped forwards.

"Basically, before they returned John to the surface they were able to suppress his memories of being transported down to the city and attached to the device. We think we can bring these memories back to the surface. Once he can remember all of this Colonel Sheppard should realise that the memories of the destruction of Atlantis are false, and that he really is home."

Elizabeth nodded slowly.

"Okay, do it." She turned away slightly, and activated her radio. "Major Lorne? This is Weir. I want additional security posted around the infirmary, we're going to try to help Colonel Sheppard."

"Copy that Ma'am. I'll have Ronon there as well."

"Good idea."

Ten minutes later the additional security officers had taken up their posts. Ronon stood a few metres away from the bed, his blaster in his hand. Elizabeth walked over to him, concerned.

"Are you alright Ronon?" He looked at her briefly, then his eyes slid back to the bed.

"He got past me once. Not going to happen again." Elizabeth started to answer, but was interrupted as Carson and Lessa wheeled the machine over to John's bed.

"We are sure that John won't get stuck in there again, right?" Rodney asked.

"Do not worry Dr Mckay. We will not be placing Colonel Sheppard into a simulation, we are merely removing the blocks which prevent him from remembering everything."

Carson took a deep breath.

"Alright, we're ready. He's waking up." Instantly, the already tense atmosphere become electric. John's eyes opened slowly.

"Colonel? John, can you here me?" Carson asked, leaning towards him. John suddenly lunged towards him, and was jerked back by the restraints as Carson stumbled back.

"Don't. Touch. Me." John snapped. Carson recovered, and stepped forwards.

"Sorry Colonel, It's for your own good." Carson nodded to two SF's standing next to the bed. They leaned over and firmly grabbed John's shoulders as he struggled.

"What are you... get off me!" Elizabeth couldn't help but stare at John as he frantically struggled. Every time his mad eyes landed on her she felt a stab of pain in her chest. Carson and Lessa quickly and carefully attached several leads to John's forehead.

"What the...No! Get off! God, help me!" Lessa activated the device, and John fell back into his bed.

"He is stable. I am starting the process." No one spoke for a few minutes, then Lessa looked up.

"It is done. He will now remember everything."

Elizabeth nodded.

"Remove the device." She was shocked by how harsh her voice sounded as her emotions threatened to overwhelm her. The machine powered down, and Lessa disconnected the leads. John started to stir again. His eyes were again wild as they opened, but this time they locked onto Lessa.

"You. What did you... a city... machine...my head. Oh God. What did you do to me?" He whispered the last few words. Lessa stepped forwards.

"We wanted to learn about your culture. We placed you in an artificial environment, but your mind took control of it and corrupted the simulation. Everything you recall of the last 6 months...did not happen." Elizabeth stepped forwards.

"Atlantis is safe, John. We're all safe." John's head snapped around, eyes boring into hers. His face froze, then melted into pure relief.

"Elizabeth?" In that moment, she forgot where she was, forgot everything apart from him. She moved forwards, brushing Lessa aside as she threw her arms around his neck. He tried to respond, but was still restrained.

The others slowly filed out of the room, leaving only Carson to watch as John quietly cried in Elizabeth's arms.

**AN:**

**Well I don't know if anyone was really that desperate to read this, but if you were I'm sorry for the long delay. Real life (pesky thing that it is) kept getting in the way. Still, better late than never, and the next and final chapter should be done soon as well (mostly because I've got yet another plot bunny, and oh boy is this a big one!)**


	6. Chapter 6

**Chapter 6**

"Colonel Sheppard seems to be making a lot of progress, but I am concerned...Dr Weir?" Elizabeth looked over to Dr Heightmeyer.

"Sorry, Kate, go on."

"Are you alright? You seem distracted." Elizabeth smiled wryly and nodded.

"I'm fine, I just haven't been getting a lot of sleep lately."

"Something you want to talk about?"

"No, I'm fine, really. Anyway, you were talking about John."

"Yes. He seems to have completely come to terms with the fact that his memories are false, however I am still concerned. I get the feeling there's something he's not telling me, and I think it might have something to do with you."

"Me? Why?" Elizabeth leaned forwards.

"I don't know. Whenever the two of you are together, or even when I mention your name, Colonel Sheppard...tenses. I really can't be more specific." Elizabeth nodded slowly.

"I know what you mean. At first I thought he was just having to adjust to reality, but it's been two weeks now and he still turns into a ball of nerves when I'm around him. I just, I wish there was someway I could help him." Kate smiled sympathetically.

"Actually, I think you can help him. If there is something he's hiding then he won't tell me. I think you could get him to open up." Elizabeth sat back in her chair.

"Are you sure? Ever since he came back to reality he's been...distant around me." Kate shrugged.

"You may be right, but I can't help him. I think you can."

Elizabeth nodded.

"Then I'll try."

SGA-SGA-SGA

Later that afternoon, Elizabeth walked into the gym. John was there, using a punching bag. She was no expert, but he seemed to be hitting the bag much harder than normal.

"John?" Even from behind she could see him tense up. She hated that.

"Hello Elizabeth." He continued to punch the bag. Elizabeth walked round the punching bag until she could see his face.

"I spoke to Dr Heightmeyer today. She says you're doing well." She winced when she realised how formal she sounded.

"That's good." He said. He still hadn't looked at her.

"She also said... She also said that she didn't think you were telling her everything. She said that she thought that you were hiding something." She paused, but he didn't respond. "Something to do with me." After that, he stopped, still avoiding her eyes. He walked over to a water cooler, and took a long drink.

"Well, she's right." Elizabeth walked over to him, and tried to put a hand on his arm, but he jerked away.

"What is it John?"

He glanced at her then, eyes briefly locking on hers, then he turned away. His voice as quiet, but controlled.

"The simulation I was placed in carried on from the real world. Everything carried on just like it would here. In the simulation, when I got back to Atlantis, you and I went to dinner." Her eyes widened as she began to understand. "It went well, and we had another, and another." He smiled slightly, but it was a tight, pained smile. "It was only three weeks before we slept together. I was terrified of pushing you too fast, in the end you had to make the first move. Two months after that I moved into your room." He finally looked up and looked at her. She had to force herself not to step back as she saw the depth of emotion in his face. "We were together for six months. I was considering asking you... Then the Wraith came. Dozens of hive ships, our shield was overwhelmed within a day. We had ordered the evacuation of the city, and when the shield collapsed only Mckay, you me and Teyla and Ronon were left." He stopped.

"What happened?" He took a deep breath, and closed his eyes briefly before continuing.

"The gate room was hit by a damaged dart. The gate was buried in rouble, no way we could dig it out, they were already inside the city. So you me Ronon and Teyla headed towards the jumper bay."

"What about Rodney?"

"The Wraith had infected the system with a virus. We couldn't initiate the self-destruct. Rodney...pushed me into the jumper bay and sealed the door. He, he stayed behind to overload the generators manually. I tried, I tried to override the door mechanism but it would work. You were pulling on my arm, trying to get me into a jumper. I came. I left him to die."

"It wasn't your fault John, you had to"

"Elizabeth." He stopped her with a raised hand. "I'm not done. After you got me into the jumper I took off, and headed for the mainland. The settlement had already been destroyed, so I aimed for the large forest. We were flying over the edge when the cloak failed. It just...stopped working. Darts were everywhere, shot us down. We all survived, but Teyla and Ronon were driven off in a different direction when the darts started to strafe us. Our radios were damaged, so you and I kept going. I don't know what I was hoping for, maybe that the Deadalus would arrive and save us, I don't know. Three days after the crash we found a cave, it was sheltered, figured it was as good a place as any to hide out. Two days later I woke up." His voice cracked "I woke up to the sound of you screaming. A Wraith had found us, and... he was feeding on you. I grabbed my P90 and emptied an entire clip into its back but it just healed. You were screaming, I only had my pistol..." His voice trailed off, tears glimmering in his eyes.

"John?"

"I shot you. Straight through the head. I killed you Elizabeth, I killed the woman I loved." He was practically choking on the words. "The Wraith turned on me, but I wasn't going to be fed on. I put the pistol to my head, and pulled the trigger. The next thing I knew, I was lying in the infirmary, and there you were." The tears were running silently down his face.

Elizabeth stood there, stunned. John continued to stare at her, then suddenly ran out of the gym. She slowly walked over to a bench and sat down. He had killed her? But, it wasn't her, not really. Of course, she reflected, that didn't matter to him.

**AN: That chapter was intended to be the last one, but I ran on a bit and figured you might as well see that whilst I try and write the (almot certainly) final** **chapter. Read and review please!**


	7. Chapter 7

**Chapter 7**

Later that night, Elizabeth walked out of the control room onto the balcony. It had not been a good day. She had tried to stay focussed on her work, but even Rodney had commented on how distracted and tired she seemed. As she stared out across the dark ocean, her thoughts irresistibly drifted back towards John, to their first argument out here, to how he had given her a birthday present (she never had learned how he knew her birthday.)

"We had our first date on this balcony." She looked round and saw John standing in the shadows. "I dragged you out of your office, brought a picnic." She couldn't help but smile at him.

"I imagine it wouldn't have been too hard to drag me away." He smiled sadly and moved forwards to lean on the rail next to her. It was stupid, but she noticed that he wasn't standing as close as he normally would.

"No. You were always the eager one. I was always scared that I'd push too hard and scare you off." Elizabeth nodded. They stood there, as the silence grew around them until it seemed to drown out the sound of the ocean. Eventually, she turned and started to leave.

"I know it wasn't real." She stopped, and turned around.

"It was real for you. I just wish..." He nodded

"I wish. I wish that I could take you out to dinner, that we could have a picnic, but"

"But you would be thinking of her. I know, and I understand."

"I don't know what I'm going to do, you know? Every time I look at you, I see her. I wish I could just forget everything, but I guess that's not an option. I just, I need some time, you know?"

Elizabeth closed her eyes briefly.

"Yeah. I guess all you can do is try to come to terms with it. I won't push you, not this time. I would like to still be your friend though, if nothing else."

He looked at her gratefully.

"I'd like that."

SGA-SGA-SGA

Months passed. John resumed his leadership of AR-1, and started getting into all sorts of trouble off-world again. In Atlantis, he was his old self again, winding up Rodney (although he also now had more respect for him), playing basketball with Ronon, Lorne and the other sport fans. He was of course still affected by his experiences, Elizabeth noticed that he usually drifted away from large groups, preferring to spend time with a few close friends. He would occasionally go "exploring", wandering the city for a few days on his own. Elizabeth would never admit it, but she always kept an eye on him using the city's scanners. Their relationship started to heal as well, but it wasn't the same. They started to eat meals together, but there was no longer any playful flirting, and they usually sat with the others. Carson in particular noticed this. He had asked her why once, and she had smiled and laughed it off, but she knew he was still worried.

There was one aspect of his life where John had not returned to normal. She overheard Rodney talking about it to Teyla once.

"I'm just saying that it's weird."

"Perhaps Colonel Sheppard has simply not been attracted to any of them."

"Are you kidding? That blonde one on our mission was amazing, and clearly interested in him, and he didn't even respond to her flirting! It's like he just isn't interested in women anymore!"

"Even if that is the case, you should respect the Colonel and stop discussing this, even with me."

"Hmm!" With that, Rodney left.

"Perhaps, Rodney," Elizabeth heard Teyla mutter to herself "he is only interested in one woman."

Around six months after John's "incident" (as most people now referred to it), Elizabeth noticed that he was unusually snappy. This continued for several days, and then it suddenly stopped. Something changed. Suddenly, they were eating meals together and it wasn't awkward. John stopped wandering off to go exploring, which irritated a lot of scientists who used to wait for him to come back with news of new areas for them to examine. Elizabeth noticed, and waited, and eventually asked him about it when they were alone in her office, doing some paperwork together.

"John?"

"Mmm?"

"What's going on?" He looked up

"Sorry?"

"Just after the...incident, you said you wanted us to be friends. For six months you've been kinda distant" she said, feeling increasing like a petulant child "and now...it's like we've suddenly gone back to normal."

"Oh. Right." John rocked back on his chair (a habit which drive her crazy, which, she suspected, made him want to do it even more).

"Has something happened?" He sighed, looking slightly embarrassed.

"Umm, actually it's that something didn't happen."

"Sorry?"

"They didn't come." She suddenly understood.

"The Wraith?"

"Yeah. In the simulation they arrived last week. I guess I kinda expected them to show up, expected it all to happen for real. Now that they haven't, I feel...free." He looked up, and she felt a sudden wave of joy sweep over her.

"You mean..." she trailed off, scared to ask him. He grinned at her.

"Wow, I've never actually seen you speechless before. Six months ago I told you I needed some time, and you understood. Now I'm ready." He stood, and extended an arm towards her. She couldn't help the idiotic smile on her face as she rose and placed her hand in his. They started to walk out of her office, ignoring the smiles of everyone in the control room.

"John?"

"Yeah?"

"Let's not have a picnic on the balcony, okay?" He smiled.

"Actually I was thinking we might watch a movie."

"Any movie in particular?"

"Well, I hear Lorne just got The Matrix..." He burst out laughing when he saw her expression.

"John, I'm going to kill you." They walked through the control room, and out into the corridor. "Oh, and John?" as he half turned towards her, she leaned towards him and kissed him lightly on the cheek, slipping an arm around his waist. "Welcome to the real world."

**AN: Huh. Nine thousand words, that's the longest story I've written in a while. Sorry there was no proper kiss at the end, I just couldn't comfortably write it in. And for those of you who haven't seen the Matrix, "Welcome to the real world is a quote". Now go and watch this fantastic film (but don't bother with the sequels!)**

** As always, I hope you enjoyed this.  
**


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